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- PDB-4eah: Crystal structure of the formin homology 2 domain of FMNL3 bound ... -

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Basic information

Entry
Database: PDB / ID: 4eah
TitleCrystal structure of the formin homology 2 domain of FMNL3 bound to actin
Components
  • Actin, alpha skeletal muscle
  • Formin-like protein 3
KeywordsPROTEIN BINDING / ATP binding / cytoskeleton / formin / FMNL3 / actin
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / RHO GTPases Activate Formins / GTPase activating protein binding / cytoskeletal motor activator activity / cortical actin cytoskeleton organization / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle ...small GTPase binding => GO:0031267 / RHO GTPases Activate Formins / GTPase activating protein binding / cytoskeletal motor activator activity / cortical actin cytoskeleton organization / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / cytoskeleton organization / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / cell migration / lamellipodium / cell body / regulation of cell shape / angiogenesis / hydrolase activity / protein domain specific binding / intracellular membrane-bounded organelle / calcium ion binding / positive regulation of gene expression / Golgi apparatus / magnesium ion binding / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Formin-like protein 3 / Formin-like protein, animal / Formin, FH2 domain / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain ...Formin-like protein 3 / Formin-like protein, animal / Formin, FH2 domain / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Armadillo-type fold / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / Actin, alpha skeletal muscle / Formin-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsThompson, M.E. / Heimsath, E.G. / Gauvin, T.J. / Higgs, H.N. / Kull, F.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: FMNL3 FH2-actin structure gives insight into formin-mediated actin nucleation and elongation.
Authors: Thompson, M.E. / Heimsath, E.G. / Gauvin, T.J. / Higgs, H.N. / Kull, F.J.
History
DepositionMar 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Actin, alpha skeletal muscle
A: Formin-like protein 3
E: Formin-like protein 3
C: Formin-like protein 3
B: Formin-like protein 3
H: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,16624
Polymers352,4298
Non-polymers2,73716
Water0
1
D: Actin, alpha skeletal muscle
A: Formin-like protein 3
E: Formin-like protein 3
G: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,58312
Polymers176,2144
Non-polymers1,3698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18080 Å2
ΔGint-78 kcal/mol
Surface area63290 Å2
MethodPISA
2
C: Formin-like protein 3
B: Formin-like protein 3
H: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,58312
Polymers176,2144
Non-polymers1,3698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18140 Å2
ΔGint-78 kcal/mol
Surface area63300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.980, 126.050, 129.620
Angle α, β, γ (deg.)90.00, 93.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 562:614 OR RESSEQ 635:937 )
211CHAIN E AND (RESSEQ 562:614 OR RESSEQ 635:937 )
311CHAIN C AND (RESSEQ 562:614 OR RESSEQ 635:937 )
411CHAIN B AND (RESSEQ 562:614 OR RESSEQ 635:937 )
112CHAIN D AND (RESSEQ 5:39 OR RESSEQ 52:372 )
212CHAIN H AND (RESSEQ 5:39 OR RESSEQ 52:372 )
312CHAIN G AND (RESSEQ 5:39 OR RESSEQ 52:372 )
412CHAIN F AND (RESSEQ 5:39 OR RESSEQ 52:372 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 42096.953 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein
Formin-like protein 3


Mass: 46010.223 Da / Num. of mol.: 4 / Fragment: FH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fmnl3, Kiaa2014 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6ZPF4
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 11% PEG 10000, 0.2 M magnesium acetate, 0.1 M MES, pH 6.5, Silver Bullet 33 (0.20% w/v D-(+)-Maltose monohydrate, 0.20% w/v D-(+)-Melibiose monohydrate, 0.20% w/v D-(+)-Raffinose ...Details: 11% PEG 10000, 0.2 M magnesium acetate, 0.1 M MES, pH 6.5, Silver Bullet 33 (0.20% w/v D-(+)-Maltose monohydrate, 0.20% w/v D-(+)-Melibiose monohydrate, 0.20% w/v D-(+)-Raffinose pentahydrate, 0.20% w/v D-(+)-Trehalose dihydrate, 0.20% w/v Stachyose hydrate, 0.02 M HEPES sodium pH 6.8), Silver Bullet 70 (0.2% w/v Anthrone, 0.2% w/v Benzidine, 0.2% w/v N-(2-Acetamido)-2-aminoethanesulfonic acid, 0.2% w/v Phenylurea, 0.2% w/v -Alanine, 0.02 M HEPES sodium pH 6.8), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2010
RadiationMonochromator: K-B pair of biomorph mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.4→19.87 Å / Num. all: 55841 / Num. obs: 55419 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.103 / Net I/σ(I): 10.74
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 3.84 % / Mean I/σ(I) obs: 2.62 / Num. unique all: 4626 / % possible all: 99.9

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHENIXAutoMRmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→19.819 Å / SU ML: 0.43 / σ(F): 1.99 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 2894 5.22 %thin shells
Rwork0.2301 ---
obs0.2325 55408 99.78 %-
all-55841 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.225 Å2 / ksol: 0.293 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.2636 Å2-0 Å21.748 Å2
2---22.9013 Å2-0 Å2
3---40.1649 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22720 0 172 0 22892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123316
X-RAY DIFFRACTIONf_angle_d1.44931500
X-RAY DIFFRACTIONf_dihedral_angle_d18.1238832
X-RAY DIFFRACTIONf_chiral_restr0.1023540
X-RAY DIFFRACTIONf_plane_restr0.0074032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2886X-RAY DIFFRACTIONPOSITIONAL
12E2886X-RAY DIFFRACTIONPOSITIONAL0.04
13C2886X-RAY DIFFRACTIONPOSITIONAL0.046
14B2886X-RAY DIFFRACTIONPOSITIONAL0.045
21D2785X-RAY DIFFRACTIONPOSITIONAL
22H2785X-RAY DIFFRACTIONPOSITIONAL0.045
23G2785X-RAY DIFFRACTIONPOSITIONAL0.041
24F2785X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.45550.33611270.28262443X-RAY DIFFRACTION100
3.4555-3.51470.33861400.2712520X-RAY DIFFRACTION100
3.5147-3.57830.34971410.27092478X-RAY DIFFRACTION100
3.5783-3.64670.33211380.2652463X-RAY DIFFRACTION100
3.6467-3.72070.33141430.25132540X-RAY DIFFRACTION100
3.7207-3.8010.30511350.25232491X-RAY DIFFRACTION100
3.801-3.88880.32091390.25062461X-RAY DIFFRACTION100
3.8888-3.98530.31881400.24212488X-RAY DIFFRACTION100
3.9853-4.09210.28661210.23512530X-RAY DIFFRACTION100
4.0921-4.21140.27961220.22062537X-RAY DIFFRACTION100
4.2114-4.3460.2591560.20762473X-RAY DIFFRACTION100
4.346-4.49950.23511620.19482472X-RAY DIFFRACTION100
4.4995-4.67740.22761280.20322501X-RAY DIFFRACTION100
4.6774-4.88730.281220.21522509X-RAY DIFFRACTION100
4.8873-5.14070.28411550.22662474X-RAY DIFFRACTION100
5.1407-5.45650.26231560.24522502X-RAY DIFFRACTION100
5.4565-5.86760.37841060.2792521X-RAY DIFFRACTION100
5.8676-6.43960.32461050.25332553X-RAY DIFFRACTION100
6.4396-7.32990.29671520.24382498X-RAY DIFFRACTION100
7.3299-9.08440.23431540.19942517X-RAY DIFFRACTION99
9.0844-19.81910.22891520.20922543X-RAY DIFFRACTION99

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